DistanceMatrix¶
- class DistanceMatrix[source]¶
A container for distances between sequences (usually).
The numbers are in self.matrix, a self.dim * self.dim list of lists.
There is also a self.names attribute, which is usually for sequence names.
- bionj()[source]¶
Use bionj to make a neighbor-joining tree, which is returned.
The resulting tree is read in by p4, and is returned.
We interact with bionj by writing files, but care is taken that existing files are not overwritten, because new file names are made to be unique.
If the branch lengths are less than zero, they are made to be zero.
- fastme()[source]¶
Use fastme to make a minimum-evolution tree, which is returned.
The resulting tree is read in by p4, and is returned.
We interact with fastme by writing files, but care is taken that existing files are not overwritten, because new file names are made to be unique.
If the branch lengths are less than zero, they are made to be zero.
- flatTriangle(upper=True)[source]¶
Get (default upper) triangle as a simple list
If arg upper is off, the lower triangle is returned.
- njUsingPaup(paupPath='paup')[source]¶
Use paup to make a neighbor-joining tree, which is returned.
The resulting tree is read in by p4, and is returned.
We interact with paup by writing files, but care is taken that existing files are not overwritten, because new file names are made to be unique.
If this does not work well, try setting the paupPath arg.